A team of researchers at The Scripps Research Institute has found that RNA riboswitches respond simultaneously to numerous metabolites rather than just a single compound as was previously believed.

Details of the study are reported in “The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo,” which appears in an advance online publication of Nature Structural and Molecular Biology.

“The study provides new insights into how a single RNA molecule can integrate both positive and negative signals from a cell,” says Martha Fedor, Ph.D., the study’s senior author and an associate professor and member of the Skaggs Institute for Chemical Biology at Scripps Research.

Dr. Fedor’s group examined the function of a type of riboswitch that binds to a metabolite called glucosamine-6-phosphate, an amino sugar required for the cell wall and other vital structures in bacterial cells. The riboswitch resides in the mRNA that carries instructions for the enzyme responsible for the production of glucosamine-6-phosphate, called GlmS.

When glucosamine-6-phosphate is abundant in a cell, the riboswitch stops production of the GlmS enzyme by destroying itself and its mRNA. But when glucosamine-6-phosphate concentrations are low, the glmS riboswitch does not self-destruct, keeping the mRNA functioning.

Dr. Fedor and graduate student Peter Watson designed an assay to measure the amounts of the glmS riboswitch in yeast cells as they added increasing concentrations of glucosamine. The scientists found that if they grew their yeast in energy-rich broth that contained glycerol, a 3-carbon energy source, the riboswitch behaved as expected, shutting off the glmS mRNA in response to increasing glucosamine concentrations. But if bacteria were grown in a broth containing glucose, a 6-carbon energy source, the riboswitch no longer self-destructed.

Dr. Fedor and Watson concluded that the riboswitch can bind both glucosamine-6-phosphate and glucose-6-phosphate, though, binding with each compound produced opposite results. Binding glucosamine-6-phosphate induces self-destruction of the riboswitch and turns the glmS gene off; binding glucose-6-phosphate prevents self-destruction and keeps the glmS gene turned on.

“Scientists had long focused on the ability of riboswitches to recognize a single compound, but we have now found that riboswitches, or at least this one, can recognize multiple ones,” notes Watson.

The glmS riboswitch function depends upon a balance between these two and possibly additional competing signals, the researchers found. “When glucose concentrations are high in a cell, it means that energy is abundant,” Watson explains. “That is when cells would want to grow and divide and make more glucosamine-6-phosphate to build new cell walls. But when glucosamine-6-phosphate concentrations are high, then cells know to stop making more of this compound.”

Dr. Fedor remarks, “This kind of complex signaling had long thought to be the domain of just proteins. This is another example of a function thought to belong only to proteins that we now know RNA can do.”

Dr. Fedor and Watson are now testing whether other types of riboswitches use this same mechanism. Until now, most known riboswitches have been found to regulate their respective mRNAs by changing their 3-D structures in response to metabolite binding.